trajolecule 1.7.0rc1

MD trajectory viewer

trajolecule: protein trajectory viewer

This viewer allows easy exploration of MD trajectories:

• hop through frames or 2d matrix view
• easy bookmarking of specific views, frames and details
• pocket discovery tool
• ligand table against a conformation
• contact map
• inter-atomic distance plots
• port mapping for remote vm's

It also prioritises fast loading, mainly by skipping solvent atoms as a default. Other viewers will be better for publication quality images.

It uses the jolecule javascript protein/DNA viewer.

Installation

uv is the best tool to install python tooling.

Note: on Mac, there may be a slow initial startup time as Rosetta transpiles some x86 libraries to ARM

1. installing with uv to make trajolecule globally available:

   >> uv tool install trajolecule
   

2. using uv to run trajolecule in an isolated environment (not in the global path):

   >> uvx trajolecule
   

3. if you want to stay in the pip ecososystem, you can install trajolecule using pipx:

   >> pipx install trajolecule
   

4. or if you want to install trajolecule in your current environment:

   >> pip install trajolecule
   

Examples

Once installed, check out the command-line options by running the command:

   >> trajolecule

I suggest downloading the examples to play with all the different modes: https://github.com/boscoh/trajolecule/tree/main/examples

Developing trajolecule

trajolecule has two components

• back-end server which is a Python fastapi backend server that reads trajectories and serves it over a local port
• front-end client that runs in the browser and displays free-energy surfaces and proteins

Building the trajolecule client in development mode

Installing javascript deps

First you must install the dependencies in rseed/rseed/jolecule/vue:

npm install

Then you must install the jolecule js repo somewhere in your system (not in the rseed directory).

In /path/to/jolecule:

npm link

Then in trajolecule/client:

npm link jolecule

Once linked, we can build the client:

npm run build

Then you need to run the build script, that will copy the client into sever/client:

./build.sh

Release Notes

• 1.7.0rc1
  • renamed to trajolecule
  • uv pyproject
  • file save fixes
  • ligands mode works well
• 1.6.11
  • more bug fixes
• 1.6.10
  • bug fixes for loading frames
• 1.6.9
  • multiple matrix
• 1.6.8
  • always strips water by default
• 1.6.7
  • autodetect sparse versus dense matrix
• 1.6.6
  • defaults to rshow.matrix.yaml
  • handles uploads of matrix json or plain matrix double list
  • popups on left adjusts
  • autodetects sparse versus full matrix in fes
• 1.6.5
  • consolidate with easytraj 0.2.5 and foamdb 0.4.0
• 1.6.4
  • import cleanup
  • logging
  • easytrajh5 0.2.3
• 1.6.3
  • import bus
• 1.6.2
  • alphaspace toggle bug
  • easytrajh5 bus
• 1.6
  • dep to easytrajh5
  • file_mode a/r detect
  • ensemble view
  • slideshow
• 1.5.2
  • distance plots
• 1.5
  • ligand focus
  • LRU fixed
  • select_min_frame
• 1.4
  • dry_topology streaming
  • reworked async calls
  • Alphaspace Radius UX - pockets panel
  • refactored Vue components
  • Vuex for state
  • hydrogen on/off option
  • profiling logging output
• 1.3.4
  • logging
• 1.3.3
  • removed FES remapper
• 1.3.2
  • deprecated FreeEnergySurface
• 1.3.1
  • removed foamdb as dep (creates pip install issues)
• 1.3
  • AS Communities
  • compatible with RSeed 2.2
• 1.2
  • frames in url query
• 1.1
  • alphaspace frame bug fix
• 1.0
  • first release

TODO

• remove ensemble
• fix home page